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Microcolinearity between a 2-cM region encompassing the grain protein content locus Gpc-6B1 on wheat chromosome 6B and a 350-kb region on rice chromosome 2

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Abstract

The conservation of the linear order (colinearity) of genetic markers along large chromosome segments in wheat and rice is well established, but less is known about the microcolinearity between both genomes at subcentimorgan distances. In this study we focused on the microcolinearity between a 2.6-cM interval flanked by markers Xcdo365 and Xucw65 on wheat chromosome 6B and rice chromosome 2. A previous study has shown that this wheat segment includes the Gpc-6B1 locus, which is responsible for large differences in grain protein content (GPC) and is the target of a positional cloning effort in our laboratories. Twenty-one recombination events between Xcdo365 and Xucw65 were found in a large segregating population (935 gametes) and used to map 17 genes selected from rice chromosome 2 in the wheat genetic map. We found a high level of colinearity between a 2.1-cM region flanked by loci Xucw75 and Xucw67 on wheat chromosome 6B and a 350-kb uninterrupted sequenced region in rice chromosome arm 2S. Colinearity between these two genomes was extended to the region proximal to Xucw67 (eight colinear RFLP markers), but was interrupted distal to Xucw75 (six non-colinear RFLP markers). Analysis of different comparative studies between rice and wheat suggests that microcolinearity is more frequently disrupted in the distal region of the wheat chromosomes. Fortunately, the region encompassing the Gpc-6B1 locus showed an excellent conservation between the two genomes, facilitating the saturation of the target region of the wheat genetic map with molecular markers. These markers were used to map the Gpc-6B1 locus into a 0.3-cM interval flanked by PCR markers Xucw79 and Xucw71, and to identify five candidate genes within the colinear 64-kb region in rice.

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References

  • Akhunov ED, Akhunov AM, Linkiewicz AM, Dubcovsky J, Hummel D, Lazo G, Chao SM, Anderson OD, David J, Qi LL, Echalier B, Gill BS, Miftahudin, Gustafson JP, La Rota M, Sorrells ME, Zhang DS, Nguyen HT, Kalavacharla V, Hossain K, Kianian SF, Peng JH, Lapitan NLV, Wennerlind EJ, Nduati V, Anderson JA, Sidhu D, Gill KS, McGuire PE, Qualset CO, Dvorak J (2003a) Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates along chromosome arms. Proc Natl Acad Sci USA 100:10836–10841

    Article  CAS  PubMed  Google Scholar 

  • Akhunov ED, Goodyear AW, Geng S, Qi LL, Echalier B, Gill BS, Miftahudin, Gustafson JP, Lazo G, Chao SM, Anderson OD, Linkiewicz AM, Dubcovsky J, La Rota M, Sorrells ME, Zhang DS, Nguyen HT, Kalavacharla V, Hossain K, Kianian SF, Peng JH, Lapitan NLV, Gonzalez-Hernandeiz JL, Anderson JA, Choi DW, Close TJ, Dilbirligi M, Gill KS, Walker-Simmons MK, Steber C, McGuire PE, Qualset CO, Dvorak J (2003b) The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Res 13:753–763

    Google Scholar 

  • Avivi L (1978) High protein content in wild tetraploid Triticum dicoccoides Korn. In: Ramanujam S (ed) Fifth international wheat genetics symposium of the Indian society of genetics and plant breeding, New Delhi, pp 372–380

  • Bennetzen JL, Ramakrishna W (2002) Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol Biol 48:821–827

    Article  CAS  PubMed  Google Scholar 

  • Brueggeman R, Rostoks N, Kudrna D, Kilian A, Han F, Chen J, Druka A, Steffenson B, Kleinhofs A (2002) The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases. Proc Natl Acad Sci USA 99:9328–9333

    Article  CAS  PubMed  Google Scholar 

  • Cenci A, Chantret N, Xy K, Gu Y, Anderson OD, Fahima T, Distelfeld A, Dubcovsky J (2003) Construction and characterization of a half million clones Bacterial Artificial Chromosome (BAC) library of durum wheat. Theoret Appl Genet 107:931–939

    Article  CAS  Google Scholar 

  • Chao S, Sharp PJ, Worland AJ, Warham EJ, Koebner RMD, Gale MD (1989) RFLP-based genetic maps of wheat homoeologous group 7 chromosomes. Theoret Appl Genet 78:495–504

    CAS  Google Scholar 

  • Devos KM, Gale MD (2000) Genome relationship: the grass model in current research. Plant Cell 12:637–646

    CAS  PubMed  Google Scholar 

  • Dubcovsky J, Dvorak J (1995) Ribosomal RNA loci: nomads in the Triticeae genomes. Genetics 140:1367–1377

    PubMed  Google Scholar 

  • Dubcovsky J, Galvez AF, Dvorak J (1994) Comparison of the genetic organization of the early salt stress response gene system in salt-tolerant Lophopyrum elongatum and salt-sensitive wheat. Theoret Appl Genet 87:957–964

    CAS  Google Scholar 

  • Dubcovsky J, Ramakrishna W, SanMiguel P, Busso C, Yan L, Shiloff B, Bennetzen J (2001) Comparative sequence analysis of colinear barley and rice BACs. Plant Physiol 125:1342–1353

    CAS  PubMed  Google Scholar 

  • Dvorak J, McGuire PE, Cassidy B (1988) Apparent sources of the A genomes of wheats inferred from the polymorphism in abundance and restriction fragment length of repeated nucleotide sequences. Genome 30:680–689

    CAS  Google Scholar 

  • Feuillet C, Keller B (1999) High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci USA 96:8265–8270

    CAS  PubMed  Google Scholar 

  • Feuillet C, Keller B (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann Bot 89:3–10

    Article  CAS  PubMed  Google Scholar 

  • Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95:1971–1974

    CAS  PubMed  Google Scholar 

  • Gill KS, Gill BS, Endo TR (1993) A Chromosome region-specific mapping strategy reveals gene-rich telomeric ends in wheat. Chromosoma 102:374–381

    CAS  Google Scholar 

  • Goff SA, Ricke D, Lan TH, Presting G, Wang RL, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchinson D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong JP, Miguel T, Paszkowski U, Zhang SP, Colbert M, Sun WL, Chen LL, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu YS, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100

    CAS  PubMed  Google Scholar 

  • Harushima Y, Yano M, Shomura P, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998) A high-density rice genetic linkage map with 2,275 markers using a single F-2 population. Genetics 148:479–494

    CAS  PubMed  Google Scholar 

  • Jia J, Devos KM, Chao S, Miller TE, Reader SM, Gale MD (1996) RFLP-based maps of the homoeologous group-6 chromosomes of wheat and their application in the tagging of Pm12, a powdery mildew resistance gene transferred from Aegilops speltoides to wheat. Theoret Appl Genet 92:559–565

    Article  CAS  Google Scholar 

  • Joppa LR, Cantrell RG (1990) Chromosomal location of genes for grain protein content of wild tetraploid wheat. Crop Sci 30:1059–1064

    CAS  Google Scholar 

  • Joppa LR, Du C, Hart GE, Hareland GA (1997) Mapping a QTL for grain protein in tetraploid wheat (Triticum turgidum L.) using a population of recombinant inbred chromosome lines. Crop Sci 37:1586–1589

    CAS  Google Scholar 

  • Khan IA, Procunier JD, Humphreys DG, Tranquilli G, Schlatter AR, Marcucci-Poltri S, Frohberg R, Dubcovsky J (2000) Development of PCR based markers for a high grain protein content gene from Triticum turgidum ssp. dicoccoides transferred to bread wheat. Crop Sci 40:518–524

    Google Scholar 

  • Kilian A, Chen J, Han F, Steffenson B, Kleinhofs A (1997) Towards map-based cloning of the barley stem rust resistance gene Rpg1 and Rpg4 using rice as an intergenomic cloning vehicle. Plant Mol Biol 35:187–195

    CAS  PubMed  Google Scholar 

  • Kurata N, Moore G, Nagamura Y, Foote T, Yano M, Minobe Y, Gale M (1994) Conservation of genome structure between rice and wheat. Bio-Technology 12:276–278

    Google Scholar 

  • Li WL, Gill BS (2002) The colinearity of the Sh2/A1 orthologous region in rice, sorghum and maize is interrupted and accompanied by genome expansion in the Triticeae. Genetics 160:1153–1162

    CAS  PubMed  Google Scholar 

  • Marino CL, Nelson JC, Lu YH, Sorrells ME, Leroy P, Lopes CR, Hart GE (1996) RFLP-based linkage maps of the homoeologous group 6 chromosomes of hexaploid wheat (Triticum aestivum L. em. Thell). Genome 39:359–366

    CAS  Google Scholar 

  • Maroof MAS, Yang GP, Biyashev RM, Maughan PJ, Zhang Q (1996) Analysis of the barley and rice genomes by comparative RFLP linkage mapping. Theoret Appl Genet 92:541–551

    Article  Google Scholar 

  • Mesfin A, Frohberg RC, Anderson JA (1999) RFLP markers associated with high grain protein from Trititcum turgidum L. var. dicoccoides introgressed into hard red spring wheat. Crop Sci 39:508–513

    CAS  Google Scholar 

  • Michaels SD, Amasino RM (1999) A robust method for detecting single-nucleotide changes as polymorphic markers by PCR. Plant J 14:381–385

    Article  Google Scholar 

  • Moore G, Devos KM, Wang Z, Gale MD (1995) Grasses, line up and form a circle. Curr Biol 5:737–739

    CAS  PubMed  Google Scholar 

  • Olmos S, Distelfeld A, Chicaiza O, Schlatter AR, Fahima T, Echenique V, Dubcovsky J (2003) Precise mapping of a locus affecting grain protein content in durum wheat. Theoret Appl Genet 107:1243–1251

    Article  CAS  Google Scholar 

  • Paterson AH, Bowers JE, Burow MD, Draye X, Elsik CG, Jiang CX, Katsar CS, Lan TH, Lin YR, Ming RG, Wright RJ (2000) Comparative genomics of plant chromosomes. Plant Cell 12:1523–1539

    CAS  PubMed  Google Scholar 

  • Roberts MA, Reader SM, Dalgliesh C, Miller TE, Foote TN, Fish LJ, Snape JW, Moore G (1999) Induction and characterization of Ph1 wheat mutants. Genetics 153:1909–1918

    CAS  PubMed  Google Scholar 

  • SanMiguel P, Ramakrishna W, Bennetzen JL, Busso CS, Dubcovsky J (2002) Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5A. Funct Integr Genom 2:70–80

    PubMed  Google Scholar 

  • Sears ER (1966) Nullisomic-tetrasomic combinations in hexaploid wheat. In: Rilly R, Lewis KR (eds) Chromosome manipulations and plant genetics. Oliver and Boyd, Edinburgh, pp 29–45

  • Sorrells ME, La Rota CM, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Miftahudin, Mahmoud A, Gustafson PP, Qi LL, Echalier BE, Gill BS, Matthews DE, Lazo GR, Chao S, Anderson OD, Edwards H, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorak J, Zhang D, Nguyen HT, Peng J, Lapitan NLV, Gonzalez-Hernandez JL, Anderson JA, Hossain KG, Kalavacharla V, Kianian SF, Choi DW, Close TJ, Dilbirligi M, Gill KS, Steber C, Walker-Simmons MK, McGuire PE, Qualset CO (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818–1827

    CAS  PubMed  Google Scholar 

  • Sutka J, Galiba G, Vagujfalvi A, Gill BS, Snape JW (1999) Physical mapping of the Vrn-A1 and Fr1 genes on chromosome 5A of wheat using deletion lines. Theoret Appl Genet 99:199–202

    Article  CAS  Google Scholar 

  • Van Deynze AE, Dubcovsky J, Gill KS, Nelson JC, Sorrells ME, Dvorak J, Gill BS, Lagudah ES, McCouch SR, Appels R (1995a) Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat. Genome 38:45–59

    Google Scholar 

  • Van Deynze AE, Nelson JC, Yglesis ES, Harrington SE, Braga DP, McCouch SR, Sorrells ME (1995b) Comparative mapping in grasses. Wheat relationships. Mol Gen Genet 248:744–754

    PubMed  Google Scholar 

  • Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100:6263–6268

    Article  CAS  PubMed  Google Scholar 

  • Young ND, Tanksley SD (1989) Restriction fragment length polymorphism maps and the concept of graphical genotypes. Theoret Appl Genet 77:95–101

    Google Scholar 

  • Yu J, Hu SN, Wang J, Wong GKS, Li SG, Liu B, Deng YJ, Dai L, Zhou Y, Zhang XQ, Cao ML, Liu J, Sun JD, Tang JB, Chen YJ, Huang XB, Lin W, Ye C, Tong W, Cong LJ, Geng JN, Han YJ, Li L, Li W, Hu GQ, Yuan LP, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp indica) [Review]. Science 296:79–92

    CAS  PubMed  Google Scholar 

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Acknowledgements

This research was supported by research grant award no. US-3224-01 from BARD, The United States-Israel Binational Agricultural Research and Development Fund; and by USDA-IFAFS competitive grant 2001-52100-11293.

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Authors and Affiliations

  1. Institute of Evolution, University of Haifa, Mount Carmel, 31905, Haifa, Israel

    Assaf Distelfeld & Tzion Fahima

  2. Department of Agronomy and Range Science, University of California, One Shields Avenue, Davis, CA 95616-8515, USA

    Cristobal Uauy, Sofia Olmos & Jorge Dubcovsky

  3. INTA EEA Pergamino, Buenos Aires, Argentina

    Ana R. Schlatter

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  1. Assaf Distelfeld
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  2. Cristobal Uauy
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  4. Ana R. Schlatter
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  6. Tzion Fahima
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Correspondence to Jorge Dubcovsky.

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Distelfeld, A., Uauy, C., Olmos, S. et al. Microcolinearity between a 2-cM region encompassing the grain protein content locus Gpc-6B1 on wheat chromosome 6B and a 350-kb region on rice chromosome 2. Funct Integr Genomics 4, 59–66 (2004). https://doi.org/10.1007/s10142-003-0097-3

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  • DOI: https://doi.org/10.1007/s10142-003-0097-3

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